R Notebook

subclasses <- c("Pvalb", "Sst", "Vip", "Lamp5", "Frem1", "Stac")

# pre-integration subclass comparison (DE genes)
for (pc in c(T, F)) {
  p <- PlotSubclassDEIntersection(subclass.markers[[1]], subclass.markers[[2]], 
                                  rownames(objs[[1]]), rownames(objs[[2]]),
                                  sample.names[[1]], sample.names[[2]],
                                  subclasses, 0.2, "E:/Transcriptomics_V1/Integration/Opossum_Mouse-P8/subclass_markers/", percentage = pc)
  print(p)
}

Warning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer range

# pre-integration type comparison (DE genes)
for (pc in c(T, F)) {
  for (sbcl in subclasses) {
    if (sbcl %in% names(type.markers[[1]]) & sbcl %in% names(type.markers[[2]])) {
      p <- PlotIdentDEIntersection(type.markers[[1]], type.markers[[2]],
                                   rownames(objs[[1]]), rownames(objs[[2]]),
                                   sample.names[[1]], sample.names[[2]],
                                   sbcl, sbcl, "type", "type", 0.2, percentage = pc)
      print(p)
    }
  }
}

sbcl_conf_plots <- PlotSubclassCrossConfusionMatrices(objs[[1]], objs[[2]], 
                                                      sample.names[[1]], sample.names[[2]], 
                                                      assay = "SCT",
                                                      subclasses, n_iters = 10, all.genes = FALSE, upsample = TRUE)

Warning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer range

print(sbcl_conf_plots[[1]])

print(sbcl_conf_plots[[2]])

subclass.labels <- c("Pvalb", "Sst", "Vip")
ident.labels <- c("type")

idnt_conf_plots <- PlotIdentCrossConfusionMatrices(objs[[1]], objs[[2]], 
                                                   sample.names[[1]], sample.names[[2]], 
                                                   assay = "SCT",
                                                   subclass.labels, ident.labels, n_iters = 10, 
                                                   ident.genes = TRUE, all.genes = FALSE, upsample = TRUE)

[1] "Using IntegrationFeatures from the Ident level..."
[1] "Using IntegrationFeatures from the Ident level..."
[1] "Using IntegrationFeatures from the Ident level..."

for (sbcl in subclass.labels) {
  for (id in ident.labels) {
    print(idnt_conf_plots[[sbcl]][[id]][["avg1"]])
    print(idnt_conf_plots[[sbcl]][[id]][["avg2"]])
  }
}

obj.integrated <- IntegrateObjects(objs[[1]], objs[[2]], resolutions = c(1, 2), nfeatures = 3000, subsample = TRUE)

PlotIntegration(obj.integrated, "species", c("integrated_snn_res.1", "integrated_snn_res.2"), subclasses)

objs.i <- SplitObject(obj.integrated, split.by = "species")

sbcl_conf_plots_i <- PlotSubclassCrossConfusionMatrices(objs.i[[1]], objs.i[[2]], 
                                                        sample.names[[1]], sample.names[[2]], 
                                                        assay = "integrated",
                                                        subclasses, n_iters = 10, all.genes = FALSE, upsample = TRUE)

Warning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer rangeWarning: NAs introduced by coercion to integer range

print(sbcl_conf_plots_i[[1]])

print(sbcl_conf_plots_i[[2]])

subclass.labels <- c("Pvalb", "Sst", "Vip")
ident.labels <- c("type")

idnt_conf_plots_i <- PlotIdentCrossConfusionMatrices(objs.i[[1]], objs.i[[2]], 
                                                     sample.names[[1]], sample.names[[2]], 
                                                     assay = "integrated",
                                                     subclass.labels, ident.labels, n_iters = 10, 
                                                     ident.genes = TRUE, all.genes = FALSE, upsample = TRUE)

[1] "Using IntegrationFeatures from the Ident level..."

Warning: Not all features provided are in this Assay object, removing the following feature(s): Ush1c, Cdh16, Aldh1a3, Exph5, Cldn11, Ndp, Grin2c, Azgp1, Plxnb3, Asb2, Dusp5, Dlk1, Vwa7, Commd1, Tnnt2, Zhx1, Tmem200c, Satl1, Rnasek, Rnase1, Ribc2, Cpz, Igfn1, 1810020O05Rik, Tmem42, Ebi3, Mael, Abcb6, Tmem182, Pudp, Cd4, Nr0b1, Ptgr1, Kdelr3, Uba52, Cnga3, Ghrh, Pbp2, Wnt9b, Tor4a, Hapln4, Cpt2, Bnc1, Chkb, Fermt1, Rnf139, Cel, Aspg, Ing4, Pdzd9, Ano7, Ikzf1, Hhip, Prnp, Nme3, Cyp27a1, Klk11, Cd5, Dscc1, Tcea3, Galnt2, Colq, Zc3h11a, Med20, Ppt2, Scn4b, Foxo4, Alox15, TinagWarning: Not all features provided are in this Assay object, removing the following feature(s): Ush1c, Cdh16, Aldh1a3, Exph5, Cldn11, Ndp, Grin2c, Azgp1, Plxnb3, Asb2, Dusp5, Dlk1, Vwa7, Commd1, Tnnt2, Zhx1, Tmem200c, Satl1, Rnasek, Rnase1, Ribc2, Cpz, Igfn1, 1810020O05Rik, Tmem42, Ebi3, Mael, Abcb6, Tmem182, Pudp, Cd4, Nr0b1, Ptgr1, Kdelr3, Uba52, Cnga3, Ghrh, Pbp2, Wnt9b, Tor4a, Hapln4, Cpt2, Bnc1, Chkb, Fermt1, Rnf139, Cel, Aspg, Ing4, Pdzd9, Ano7, Ikzf1, Hhip, Prnp, Nme3, Cyp27a1, Klk11, Cd5, Dscc1, Tcea3, Galnt2, Colq, Zc3h11a, Med20, Ppt2, Scn4b, Foxo4, Alox15, Tinag

[1] "Using IntegrationFeatures from the Ident level..."
[1] "Using IntegrationFeatures from the Ident level..."

for (sbcl in subclass.labels) {
  for (id in ident.labels) {
    print(idnt_conf_plots_i[[sbcl]][[id]][["avg1"]])
    print(idnt_conf_plots_i[[sbcl]][[id]][["avg2"]])
  }
}

objs.m <- MapObjects(objs.i[[1]], objs.i[[2]], c("subclass", "type"), assay = "integrated")

PlotMapping(objs.m, ident.order = subclasses)